|
| Status |
Public on Dec 08, 2020 |
| Title |
B cell activation 33 hours 2 |
| Sample type |
SRA |
| |
|
| Source name |
Activated B cells
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57BL/6
activation time after lps stimulation: 33 hours (imminent division)
|
| Treatment protocol |
Naïve B cells were negatively isolated (Miltenyi, 130-090-862), CTV labelled and stimulated with 25μg/ml LPS (Salmonella typhosa origin, Sigma)
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cells were fixed with formaldehyde as described by Rao et al (Cell 2014; PMID: 25497547)
In situ Hi-C was performed as described by Rao et al (Cell 2014; PMID: 25497547).
|
| |
|
| Library strategy |
Hi-C |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
Reads pairs from each sample were aligned to the mouse genome and counted into 50 kB bin pairs using the R package diffHic v1.9.1.
Genome_build: mm10
Supplementary_files_format_and_content: Processed data files give the number of reads supporting each interaction, where an interaction corresponds to a pair of 50 kB bins. The .mtx files are space-delimited text files in Matrix Market Exchange format with integer entries. The first two columns give the indices of the two interacting genomic bins and the third column gives the read count. Bin pairs with no reads are omitted. The indices correspond to rows of the BED format file GenomicRegions.bed.gz. The processed data files can be read into R using the readMTX2IntSet function of the diffHic package or the readMM function of the Matrix package.
|
| |
|
| Submission date |
Mar 24, 2020 |
| Last update date |
Dec 08, 2020 |
| Contact name |
Gordon K Smyth |
| E-mail(s) |
smyth@wehi.edu.au
|
| Phone |
(+61 3) 9345 2326
|
| Fax |
(+61 3) 9347 0852
|
| URL |
http://www.wehi.edu.au
|
| Organization name |
Walter and Eliza Hall Institute of Medical Research
|
| Department |
Bioinformatics
|
| Lab |
Smyth
|
| Street address |
1G Royal Pde
|
| City |
Parkville |
| State/province |
Vic |
| ZIP/Postal code |
3052 |
| Country |
Australia |
| |
|
| Platform ID |
GPL19057 |
| Series (2) |
| GSE147467 |
In situ HiC of primary mouse B cell progenitor populations after activation with LPS |
| GSE147497 |
RNA-seq and in situ Hi-C of primary mouse B cell progenitor populations after activation with LPS |
|
| Relations |
| BioSample |
SAMN14441444 |
| SRA |
SRX7983466 |
